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2. Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

Author

Jurgensen, Sophie K, Roux, Simon, Schwenck, Sarah M, Stewart, Frank J, Sullivan, Matthew B, and Brum, Jennifer R

Subjects
Microbiology, Biological Sciences, Ecology, Infectious Diseases, Infection, Life Below Water, Microbiota, Oxygen, Seawater, Viruses, Water, Environmental Sciences, Technology, Biological sciences, Environmental sciences
Abstract

Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.

Published
2022

3. Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state.

Author

Jurgensen, Sophie K, Roux, Simon, Schwenck, Sarah M, Stewart, Frank J, Sullivan, Matthew B, and Brum, Jennifer R

Subjects
Infection, Microbiology, Environmental Sciences, Biological Sciences, Technology
Abstract

Microbial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.

Published
2021

4. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J, Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R, Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B, Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, and Jaillon, Olivier

Subjects
Genetics, Life Below Water, Atmospheric Sciences, Geochemistry, Oceanography, Meteorology & Atmospheric Sciences
Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.

Published
2019

6. Host-linked soil viral ecology along a permafrost thaw gradient

Author

Emerson, Joanne B, Roux, Simon, Brum, Jennifer R, Bolduc, Benjamin, Woodcroft, Ben J, Jang, Ho Bin, Singleton, Caitlin M, Solden, Lindsey M, Naas, Adrian E, Boyd, Joel A, Hodgkins, Suzanne B, Wilson, Rachel M, Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B, Wrighton, Kelly C, Crill, Patrick M, Chanton, Jeffrey P, Saleska, Scott R, Tyson, Gene W, Rich, Virginia I, and Sullivan, Matthew B

Subjects
Infectious Diseases, Aetiology, 2.2 Factors relating to the physical environment, Infection, Climate Action, Bacteria, Carbon, Carbon Cycle, Climate Change, Ecosystem, Gene Expression Profiling, Genome, Viral, Glycoside Hydrolases, Host Specificity, Permafrost, Phylogeny, Soil Microbiology, Sweden, Viral Proteins, Viruses, Microbiology, Medical Microbiology
Abstract

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1-7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8-10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

Published
2018

7. Putative archaeal viruses from the mesopelagic ocean

Author

Vik, Dean R, Roux, Simon, Brum, Jennifer R, Bolduc, Ben, Emerson, Joanne B, Padilla, Cory C, Stewart, Frank J, and Sullivan, Matthew B

Subjects
Genetics, 2.2 Factors relating to the physical environment, Aetiology, Infection, Life Below Water, Oxygen Minimum Zone, Archaeal Virus, Archaea, Oxygen, Temperature, Thermoplasmata, Biological Sciences, Medical and Health Sciences
Abstract

Oceanic viruses that infect bacteria, or phages, are known to modulate host diversity, metabolisms, and biogeochemical cycling, while the viruses that infect marine Archaea remain understudied despite the critical ecosystem roles played by their hosts. Here we introduce "MArVD", for Metagenomic Archaeal Virus Detector, an annotation tool designed to identify putative archaeal virus contigs in metagenomic datasets. MArVD is made publicly available through the online iVirus analytical platform. Benchmarking analysis of MArVD showed it to be >99% accurate and 100% sensitive in identifying the 127 known archaeal viruses among the 12,499 viruses in the VirSorter curated dataset. Application of MArVD to 10 viral metagenomes from two depth profiles in the Eastern Tropical North Pacific (ETNP) oxygen minimum zone revealed 43 new putative archaeal virus genomes and large genome fragments ranging in size from 10 to 31 kb. Network-based classifications, which were consistent with marker gene phylogenies where available, suggested that these putative archaeal virus contigs represented six novel candidate genera. Ecological analyses, via fragment recruitment and ordination, revealed that the diversity and relative abundances of these putative archaeal viruses were correlated with oxygen concentration and temperature along two OMZ-spanning depth profiles, presumably due to structuring of the host Archaea community. Peak viral diversity and abundances were found in surface waters, where Thermoplasmata 16S rRNA genes are prevalent, suggesting these archaea as hosts in the surface habitats. Together these findings provide a baseline for identifying archaeal viruses in sequence datasets, and an initial picture of the ecology of such viruses in non-extreme environments.

Published
2017

8. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

Author

Roux, Simon, Brum, Jennifer R, Dutilh, Bas E, Sunagawa, Shinichi, Duhaime, Melissa B, Loy, Alexander, Poulos, Bonnie T, Solonenko, Natalie, Lara, Elena, Poulain, Julie, Pesant, Stéphane, Kandels-Lewis, Stefanie, Dimier, Céline, Picheral, Marc, Searson, Sarah, Cruaud, Corinne, Alberti, Adriana, Duarte, Carlos M, Gasol, Josep M, Vaqué, Dolors, Tara Oceans Coordinators, Bork, Peer, Acinas, Silvia G, Wincker, Patrick, and Sullivan, Matthew B

Subjects
Tara Oceans Coordinators, Viruses, Sulfur, DNA, Viral, Ecology, Ecosystem, Seawater, Genes, Viral, Genome, Viral, Expeditions, Oceans and Seas, Metagenome, Metagenomics, Nitrogen Cycle, Geographic Mapping, Datasets as Topic, General Science & Technology
Abstract

Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.

Published
2016

9. Plankton networks driving carbon export in the oligotrophic ocean

Author

Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Subjects
Aquatic Organisms, Carbon, Chlorophyll, Dinoflagellida, Ecosystem, Expeditions, Genes, Bacterial, Genes, Viral, Geography, Oceans and Seas, Photosynthesis, Plankton, Seawater, Synechococcus, Tara Oceans coordinators, General Science & Technology
Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2016

10. Illuminating structural proteins in viral “dark matter” with metaproteomics

Author

Brum, Jennifer R, Ignacio-Espinoza, J Cesar, Kim, Eun-Hae, Trubl, Gareth, Jones, Robert M, Roux, Simon, VerBerkmoes, Nathan C, Rich, Virginia I, and Sullivan, Matthew B

Subjects
Infection, Marine Biology, Proteomics, Viral Structural Proteins, Viruses, viruses, marine, proteins
Abstract

Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.

Published
2016

14. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author

Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean-Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), University of British Columbia (UBC), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Dipartimento di Fisica e Astronomia 'Galileo Galilei', Università degli Studi di Padova = University of Padua (Unipd), Consorzio Nazionale Interuniversitario per le Scienze FIsiche della Materia (CNISM), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Institut de Biologie François JACOB (JACOB), Ohio State University [Columbus] (OSU), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Maine, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), French National Research Agency (ANR)HYDROGEN/ANR-14CE23-0001, National Science Foundation (NSF)OCE-1536989, OCE-1829831, Commissariat a l'Energie Atomique et aux Energies Alternatives, Graphene Flagship, European Project: 634486,H2020,H2020-BG-2014-2,INMARE(2015), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Universita degli Studi di Padova, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Centre de Mathématiques et de Leurs Applications (CMLA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Infectiologie Santé Publique (ISP-311), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Institut Pprime (PPRIME), Université de Poitiers-ENSMA-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
010504 meteorology & atmospheric sciences, Biogeography, Oceans and Seas, Context (language use), 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, plankton biogeography, genomics, Ecosystem, genetics, 14. Life underwater, microbial oceanography, 030304 developmental biology, 0105 earth and related environmental sciences, Seascape, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, metagenomics, General Immunology and Microbiology, Geography, General Neuroscience, Ocean current, fungi, Community structure, General Medicine, 15. Life on land, Plankton, Oceanography, 13. Climate action, Metagenomics, metabarcoding, ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton., We thank the commitment of the following people and sponsors who made this expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Paris Sciences et Lettres (PSL) Research University (ANR-11-IDEX-0001–02), the French Government ANR (projects FRANCE GENOMIQUE/ANR-10-INBS-09, MEMO LIFE/ANR-10-LABX-54, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, MAPPI/ANR-2010-COSI-004, TARA-GIRUS/ANR-09-PCS-GENM-218), US NSF grant DEB-1031049, FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. The bulk of genomic computations were performed using the Airain HPC machine provided through GENCI- [TGCC/CINES/IDRIS] (grants t2011076389, t2012076389, t2013036389, t2014036389, t2015036389 and t2016036389). We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted us sampling permissions.

Published
2022
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17. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author

Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, and Tara Oceans Coordinators

Abstract

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

Published
2022

18. Show and tell: approaches for effective figures.

Author

Midway, Stephen R., Brum, Jennifer R., and Robertson, Matthew

Subjects
*SCIENTIFIC ability, *MANAGEMENT information systems, *SCIENTIFIC communication, *HUMAN-computer interaction
Abstract

Humans are visual beings, and everything we look at initiates a cascade of cognitive reactions that hopefully ends in information transfer and understanding. In summary, although there are many potential cognitive biases that may influence figure interpretation ( I see i Dimara et al. [6] for a review), the most common biases can be alleviated by choosing figure designs that match the underlying data, representing data along meaningful and consistent axis ranges, and ensuring that figure element differences are easily discernable. The same goes for figures - visual information risks not being transmitted if visual elements are not used effectively, but simply being able to effectively construct a figure doesn't mean you have relevant information to share. 1a all extraneous information is absent, thus reducing the I foreground effect i in which the viewer may focus on only some visual information and come to an inaccurate conclusion (Stone et al. [24]). [Extracted from the article]

Published
2023
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21. A genomic catalog of Earth’s microbiomes

Author

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, IMG/M Data Consortium, Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, and IMG/M Data Consortium

Abstract

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Published
2021

22. Data from: Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author

Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean‐Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, and Tara Oceans Coordinators

Abstract

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the 'seascape') by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

Published
2021

23. 5m intervals of CTD profiles from R/V New Horizon cruise NH1315 in the Eastern Tropical North Pacific (ETNP) during June 2013

Author

Brum, Jennifer R. and Brum, Jennifer R.

Abstract

Dataset: ETNP CTD casts 5m intervals, 5m intervals of CTD profiles from R/V New Horizon cruise NH1315 in the Eastern Tropical North Pacific (ETNP) during June 2013. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/822818, NSF Division of Ocean Sciences (NSF OCE) OCE-1658040

Published
2020

24. Estimated frequency of lytic viral infection from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013

Author

Brum, Jennifer R. and Brum, Jennifer R.

Abstract

Dataset: ETNP Frequency of Lytic Viral Infection, Estimated frequency of lytic viral infection from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 from 13-28 June 2013. Samples were deposited onto TEM grids, stained, and examined using a transmission electron microscope. Micrographs of cells were collected and characterized as infected or uninfected. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/822914, NSF Division of Ocean Sciences (NSF OCE) OCE-1658040

Published
2020

25. Morphotypes, capsid widths, and tail lengths of viruses from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013

Author

Brum, Jennifer R. and Brum, Jennifer R.

Abstract

Dataset: ETNP Viral Morphology, Morphotypes, capsid widths, and tail lengths of viruses in samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 from 13-28 June 2013. Viruses were deposited onto TEM grids, positively stained, and examined using a transmission electron microscope. Micrographs were collected and characterized by morphotype, as well as measured using ImageJ software. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/823131, NSF Division of Ocean Sciences (NSF OCE) OCE-1658040

Published
2020

26. Accession numbers of viral metagenomes from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 during June 2013

Author

Brum, Jennifer R. and Brum, Jennifer R.

Abstract

Dataset: ETNP Viromes, Accession numbers of viral metagenomes from samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 from 13-28 June 2013. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/823295, NSF Division of Ocean Sciences (NSF OCE) OCE-1658040

Published
2020

27. Estimated abundances of viruses and bacteria determined in samples collected in the Eastern Tropical North Pacific (ETNP) on R/V New Horizon cruise NH1315 during June 2013

Author

Brum, Jennifer R. and Brum, Jennifer R.

Abstract

Dataset: ETNP Microbial Abundances, Estimated abundances of viruses and bacteria via epifluorescence microscopy of samples collected in the Eastern Tropical North Pacific oxygen minimum zone region (ETNP OMZ) on R/V New Horizon cruise NH1315 from 13-28 June 2013. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/823094, NSF Division of Ocean Sciences (NSF OCE) OCE-1658040

Published
2020

28. Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Karp‐Boss, Lee, Wincker, Patrick, Kandels‐Lewis, Stefanie, Jaillon, Olivier, Iudicone, Daniele, Hingamp, Pascal, Grimsley, Nigel, Gorsky, Gabriel, Follows, Michael J., Vargas, Colomban, Bowler, Chris, Boss, Emmanuel, Bork, Peer, Acinas, Silvia G., Karsenti, Eric, Weissenbach, Jean, Velayoudon, Didier, Sunagawa, Shinichi, Sullivan, Matthew B., Stemmann, Lars, Speich, Sabrina, Sieracki, Mike, Sardet, Christian, Reynaud, Emmanuel G., Raes, Jeroen, Pesant, Stéphane, Ogata, Hiroyuki, Not, Fabrice, Krzic, Uros, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Sprovieri, Mario, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Searson, Sarah, Dimier, Céline, Picheral, Marc, Guidi, Lionel, Sordino, Paolo, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, d'Alcalà, Maurizio Ribera, Stazione Zoologica Anton Dohrn (SZN), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Oceanography and Coastal Sciences, Louisiana State University (LSU), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Instituto de Engenharia de Sistemas e Computadores (INESC), Departament de Genetica, Facultat de Biologia, Universitat de Barcelona (UB), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (CAS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Istituto per l'Ambiente Marino Costiero, Sezione Ecologia Marina Integrata, European Molecular Biology Laboratory [Heidelberg] (EMBL), National Cardiovascular Center, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), University of Maine, Department of Earth and Environment [Boston], Boston University [Boston] (BU), Department of Earth Ocean and Ecological Sciences [Liverpool], University of Liverpool, Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, National Science Foundation [Arlington] (NSF), DVIPC, ANR-17-CE02-0014,CINNAMON,Analyse multi-échelle de l'adaptation à la carence en Fer chez un organisme clé du phytoplancton marin, dans un contexte de changement global(2017), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne (UNIL), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Consiglio Nazionale delle Ricerche [Roma] (CNR), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Vrije Universiteit Brussel (VUB), Department of Structural Biology, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, and JAMET, Jean-Louis

Subjects
0106 biological sciences, Atmospheric Science, PROCHLOROCOCCUS, 010504 meteorology & atmospheric sciences, Iron fertilization, species networks, DIVERSITY, PROTEIN, Oceanography, 01 natural sciences, CARBON, Settore BIO/13 - Biologia Applicata, oxidative stress, Meteorology & Atmospheric Sciences, Geosciences, Multidisciplinary, OXIDATIVE STRESS, ComputingMilieux_MISCELLANEOUS, GENE-EXPRESSION, General Environmental Science, Global and Planetary Change, LIMITATION, Ecology, IN-SITU, system biology, Geology, Plankton, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], iron response, meta-omics, MARINE-PHYTOPLANKTON, in-situ, limitation, Physical Sciences, Life Sciences & Biomedicine, Biogeochemical cycle, PACIFIC, Environmental Sciences & Ecology, Context (language use), prochlorococcus, Biology, Zooplankton, marine-phytoplankton, diversity, Atmospheric Sciences, Phytoplankton, pacific, Genetics, Environmental Chemistry, Ecosystem, 14. Life underwater, Life Below Water, 0105 earth and related environmental sciences, Science & Technology, 010604 marine biology & hydrobiology, carbon, fungi, Pelagic zone, gene-expression, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Geochemistry, Cardiovascular and Metabolic Diseases, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, protein, Environmental Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

29 pages, 9 figures, supporting information https://doi.org/10.1029/2018GB006022, Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment, We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280, the Mission Pour l'Interdisciplinarité – Project MEGALODOM, and the Fédération de Recherche GO‐SEE FR2022), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Government “Investissements d'Avenir” programs Oceanomics (ANR‐11‐BTBR‐0008), MEMO LIFE (ANR‐10‐LABX‐54), PSL* Research University (ANR‐11‐IDEX‐0001‐02), and FRANCE GENOMIQUE (ANR‐10‐INBS‐09), Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects “PHYTBACK/ANR‐2010‐1709‐01,” POSEIDON/ANR‐09‐BLAN‐0348, PROMETHEUS/ANR‐09‐PCS‐GENM‐217, TARA‐GIRUS/ANR‐09‐PCS‐GENM‐218, SAMOSA/ANR‐13‐ADAP‐0010, CINNAMON/ANR‐17‐CE02‐0014‐01), EU FP7 (MicroB3/No. 287589), ERC Advanced Grant Award (Diatomite: 294823), the LouisD foundation of the Institut de France, a Radcliffe Institute Fellowship from Harvard University to C. B., JSPS/MEXT KAKENHI (26430184, 16H06437, and 16KT0020), The Canon Foundation (203143100025), Gordon and Betty Moore Foundation (award #3790) and the US National Science Foundation (awards OCE#1536989 and OCE#1829831) to MBS, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Fonds Français pour l'Environnement Mondial, the TARA schooner and its captain and crew.

Published
2019
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29. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J., Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, Jaillon, Olivier, Karp‐Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, Weissenbach, Jean, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J., Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, Jaillon, Olivier, Karp‐Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, and Weissenbach, Jean

Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment. © 2019. American Geophysical Union. All Rights Reserved.

Published
2019

30. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sebastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima-Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, M. G., Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, R., Speich, Sabrina, Sprovieri, M., Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban de, Follows, Michael J., Grimsley, Nigel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, D'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, Ribera d’Alcalà, Maurizio, Wincker, Patrick, Bowler, Chris, Guidi, Lionel, Iudicone, Daniele, Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sebastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima-Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, M. G., Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, R., Speich, Sabrina, Sprovieri, M., Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban de, Follows, Michael J., Grimsley, Nigel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, D'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, Ribera d’Alcalà, Maurizio, Wincker, Patrick, Bowler, Chris, Guidi, Lionel, and Iudicone, Daniele

Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment

Published
2019

31. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Author

Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Romac, Sarah, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frederick, Gas, Shahinaz, Guy, Julie, Haquelle, Maud, Jacoby, E'Krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaelle, Wessner, Mark, Acinas, Silvia G., Royo-llonch, Marta, Cornejo-castillo, Francisco M., Logares, Ramiro, Fernandez-gomez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Ten Hoopen, Petra, De Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Duhaime, Melissa B., Poulos, Bonnie T., Hurwitz, Bonnie L., Pesant, Stephane, Karsenti, Eric, Wincker, Patrick, Bork, Peer, Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Hingamp, Pascal, Iudicone, Daniele, Karp-boss, Lee, Not, Fabrice, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Bazire, Pascal, Beluche, Odette, Besnard-gonnet, Marielle, Bordelais, Isabelle, Boutard, Magali, Dubois, Maria, Dumont, Corinne, Ettedgui, Evelyne, Fernandez, Patricia, Garcia, Esperance, Aiach, Nathalie Giordanenco, Guerin, Thomas, Hamon, Chadia, Brun, Elodie, Lebled, Sandrine, Lenoble, Patricia, Louesse, Claudine, Mahieu, Eric, Mairey, Barbara, Martins, Nathalie, Megret, Catherine, Milani, Claire, Muanga, Jacqueline, Orvain, Celine, Payen, Emilie, Perroud, Peggy, Petit, Emmanuelle, Robert, Dominique, Ronsin, Murielle, and Vacherie, Benoit

Subjects
fungi
Abstract

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www. ebi. ac. uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

Published
2017

33. Host-linked soil viral ecology along a permafrost thaw gradient

Author

Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Soden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frokings, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia, Sullivan, Matthew B., Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Soden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frokings, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia, and Sullivan, Matthew B.

Abstract

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood(1-7). The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans(8-10), remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

Published
2018
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34. Plankton networks driving carbon export in the oligotrophic ocean

Author

Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R., Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G., Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B., Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Gorsky, Gabriel, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R., Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G., Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B., Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2018

35. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Author

Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Duhaime, Melissa, Romac, Sarah, Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-Marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frédérick, Gas, Shahinaz, Guy, Julie, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Bazire, Pascal, Beluche, Odette, Bertrand, Laurie, Besnard-Gonnet, Marielle, Bordelais, Isabelle, Boutard, Magali, Dubois, Maria, Dumont, Corinne, Ettedgui, Evelyne, Fernandez, Patricia, Garcia, Espérance, Aiach, Nathalie Giordanenco, Guerin, Thomas, Hamon, Chadia, Brun, Elodie, Lebled, Sandrine, Lenoble, Patricia, Louesse, Claudine, Mahieu, Eric, Mairey, Barbara, Martins, Nathalie, Megret, Catherine, Milani, Claire, Muanga, Jacqueline, Orvain, Céline, Payen, Emilie, Perroud, Peggy, Petit, Emmanuelle, Robert, Dominique, Ronsin, Murielle, Vacherie, Benoit, Acinas, Silvia G., Royo-Llonch, Marta, Cornejo-Castillo, Francisco M., Logares, Ramiro, Fernández-Gómez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Hoopen, Petra Ten, De Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-Lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Poulos, Bonnie T., Hurwitz, Bonnie L., Bork, Peer, Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Pesant, Stéphane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Duhaime, Melissa, Romac, Sarah, Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-Marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frédérick, Gas, Shahinaz, Guy, Julie, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Bazire, Pascal, Beluche, Odette, Bertrand, Laurie, Besnard-Gonnet, Marielle, Bordelais, Isabelle, Boutard, Magali, Dubois, Maria, Dumont, Corinne, Ettedgui, Evelyne, Fernandez, Patricia, Garcia, Espérance, Aiach, Nathalie Giordanenco, Guerin, Thomas, Hamon, Chadia, Brun, Elodie, Lebled, Sandrine, Lenoble, Patricia, Louesse, Claudine, Mahieu, Eric, Mairey, Barbara, Martins, Nathalie, Megret, Catherine, Milani, Claire, Muanga, Jacqueline, Orvain, Céline, Payen, Emilie, Perroud, Peggy, Petit, Emmanuelle, Robert, Dominique, Ronsin, Murielle, Vacherie, Benoit, Acinas, Silvia G., Royo-Llonch, Marta, Cornejo-Castillo, Francisco M., Logares, Ramiro, Fernández-Gómez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Hoopen, Petra Ten, De Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-Lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Poulos, Bonnie T., Hurwitz, Bonnie L., Bork, Peer, Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Pesant, Stéphane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, and Wincker, Patrick

Abstract

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

Published
2018

36. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, and Iudicone, Daniele

Subjects
fungi
Abstract

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic., プランクトンの世界 : 新しいフロンティア -タラ海洋探査からの最新情報-. 京都大学プレスリリース. 2015-05-22.

Published
2015

37. Patterns and ecological drivers of ocean viral communities

Author

Brum, Jennifer R, Ignacio-Espinoza, J Cesar, Roux, Simon, Doulcier, Guilhem, Acinas, Silvia G, Alberti, Adriana, Chaffron, Samuel, Cruaud, Corinne, de Vargas, Colomban, Gasol, Josep M, Gorsky, Gabriel, Gregory, Ann C, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulos, Bonnie T, Schwenck, Sarah M, Speich, Sabrina, Dimier, Celine, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Tara Oceans Coordinators, Bork, Peer, Bowler, Chris, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, and Sullivan, Matthew B

Subjects
viruses, fungi
Abstract

Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity., プランクトンの世界 : 新しいフロンティア -タラ海洋探査からの最新情報-. 京都大学プレスリリース. 2015-05-22.

Published
2015

38. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Author

70291432, Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Romac, Sarah, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-Marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frédérick, Gas, Shahinaz, Guy, Julie, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Acinas, Silvia G., Royo-Llonch, Marta, Cornejo-Castillo, Francisco M., Logares, Ramiro, Fernández-Gómez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Hoopen, Petra Ten, De Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-Lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Duhaime, Melissa B., Poulos, Bonnie T., Hurwitz, Bonnie L., Pesant, Stéphane, Karsenti, Eric, Wincker, Patrick, 70291432, Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Romac, Sarah, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-Marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frédérick, Gas, Shahinaz, Guy, Julie, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Acinas, Silvia G., Royo-Llonch, Marta, Cornejo-Castillo, Francisco M., Logares, Ramiro, Fernández-Gómez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Hoopen, Petra Ten, De Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-Lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Duhaime, Melissa B., Poulos, Bonnie T., Hurwitz, Bonnie L., Pesant, Stéphane, Karsenti, Eric, and Wincker, Patrick

Abstract

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.

Published
2017

39. Patterns and ecological drivers of ocean viral communities

Author

Brum, Jennifer R., Gasol, Josep M., Gorsky, Gabriel, Gregory, Ann C., Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulos, Bonnie T., Ignacio-Espinoza, J. Cesar, Schwenck, Sarah M., Speich, Sarah, Dimier, Celine, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Bork, Peer, Bowler, Chris, Sunagawa, Shinichi, Wincker, Patrick, Roux, Simon, Karsenti, Eric, Sullivan, Matthew B., Doulcier, Guilhem, Acinas, Silvia G., Alberti, Adriana, Chaffron, Samuel, Cruaud, Corinne, and de Vargas, Colomban

Subjects
viruses, fungi
Abstract

Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.

Published
2015

41. Plankton networks driving carbon export in the oligotrophic ocean.

Author

70291432, Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Tara Oceans Consortium Coordinators, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Gorsky, Gabriel, 70291432, Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Tara Oceans Consortium Coordinators, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2016

42. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Roux, Simon, Brum, Jennifer R, Dutilh, Bas E, Sunagawa, Shinichi, Duhaime, Melissa B, Loy, Alexander, Poulos, Bonnie T, Solonenko, Natalie, Lara, Elena, Poulain, Julie, Pesant, Stéphane, Kandels-Lewis, Stefanie, Dimier, Céline, Picheral, Marc, Searson, Sarah, Cruaud, Corinne, Alberti, Adriana, Duarte, Carlos M, Gasol, Josep M, Vaqué, Dolors, Tara Oceans Coordinators, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Roux, Simon, Brum, Jennifer R, Dutilh, Bas E, Sunagawa, Shinichi, Duhaime, Melissa B, Loy, Alexander, Poulos, Bonnie T, Solonenko, Natalie, Lara, Elena, Poulain, Julie, Pesant, Stéphane, Kandels-Lewis, Stefanie, Dimier, Céline, Picheral, Marc, Searson, Sarah, Cruaud, Corinne, Alberti, Adriana, Duarte, Carlos M, Gasol, Josep M, Vaqué, Dolors, and Tara Oceans Coordinators

Published
2016

44. Patterns and ecological drivers of ocean viral communities.

Author

70291432, Brum, Jennifer R, Ignacio-Espinoza, J Cesar, Roux, Simon, Doulcier, Guilhem, Acinas, Silvia G, Alberti, Adriana, Chaffron, Samuel, Cruaud, Corinne, de Vargas, Colomban, Gasol, Josep M, Gorsky, Gabriel, Gregory, Ann C, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulos, Bonnie T, Schwenck, Sarah M, Speich, Sabrina, Dimier, Celine, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Tara Oceans Coordinators, Bork, Peer, Bowler, Chris, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Sullivan, Matthew B, 70291432, Brum, Jennifer R, Ignacio-Espinoza, J Cesar, Roux, Simon, Doulcier, Guilhem, Acinas, Silvia G, Alberti, Adriana, Chaffron, Samuel, Cruaud, Corinne, de Vargas, Colomban, Gasol, Josep M, Gorsky, Gabriel, Gregory, Ann C, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulos, Bonnie T, Schwenck, Sarah M, Speich, Sabrina, Dimier, Celine, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Tara Oceans Coordinators, Bork, Peer, Bowler, Chris, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, and Sullivan, Matthew B

Abstract

Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.

Published
2015

45. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Author

70291432, Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, Iudicone, Daniele, 70291432, Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, and Iudicone, Daniele

Abstract

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

Published
2015

50. A SALTY DIVIDE WITHIN ASLO?

Author

Kavanaugh, Maria T., primary, Holtgrieve, Gordon W., additional, Baulch, Helen, additional, Brum, Jennifer R., additional, Cuvelier, Marie L., additional, Filstrup, Christopher T., additional, Nickols, Kerry J., additional, and Small, Gaston E., additional

Published
2013
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